Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish

Background How and why animals lose eyesight during adaptation to the dark and food-limited cave environment has puzzled biologists since the time of Darwin. More recently, several different adaptive hypotheses have been proposed to explain eye degeneration based on studies in the teleost Astyanax mexicanus, which consists of blind cave-dwelling (cavefish) and sighted surface-dwelling (surface fish) forms. One of these hypotheses is that eye regression is the result of indirect selection for constructive characters that are negatively linked to eye development through the pleiotropic effects of Sonic Hedgehog (SHH) signaling. However, subsequent genetic analyses suggested that other mechanisms also contribute to eye regression in Astyanax cavefish. Here, we introduce a new approach to this problem by investigating the phenotypic and genetic relationships between a suite of non-visual constructive traits and eye regression. Results Using quantitative genetic analysis of crosses between surface fish, the Pachón cavefish population and their hybrid progeny, we show that the adaptive vibration attraction behavior (VAB) and its sensory receptors, superficial neuromasts (SN) specifically found within the cavefish eye orbit (EO), are genetically correlated with reduced eye size. The quantitative trait loci (QTL) for these three traits form two clusters of congruent or overlapping QTL on Astyanax linkage groups (LG) 2 and 17, but not at the shh locus on LG 13. Ablation of EO SN in cavefish demonstrated a major role for these sensory receptors in VAB expression. Furthermore, experimental induction of eye regression in surface fish via shh overexpression showed that the absence of eyes was insufficient to promote the appearance of VAB or EO SN. Conclusions We conclude that natural selection for the enhancement of VAB and EO SN indirectly promotes eye regression in the Pachón cavefish population through an antagonistic relationship involving genetic linkage or pleiotropy among the genetic factors underlying these traits. This study demonstrates a trade-off between the evolution of a non-visual sensory system and eye regression during the adaptive evolution of Astyanax to the cave environment

Using multi-group confirmatory factor analysis to evaluate cross-cultural research: Identifying and understanding non-invariance

Multi-group group confirmatory factor analysis (MGCFA) allows researchers to determine whether a research inventory elicits similar response patterns across samples. If statistical equivalence in responding is found, then scale score comparisons become possible and samples can be said to be from the same population. This paper illustrates the use of MGCFA by examining survey results relating to practicing teachers’ conceptions of feedback in two very different jurisdictions (Louisiana, USA, n=308; New Zealand, n=518), highlighting challenges which can occur when conducting this kind of cross-cultural research. As the two contexts had very different policies and practices around educational assessment, it was considered possible that a common research inventory may elicit non-equivalent responding, leading to non-invariance. Independent models for each group and a joint model for all participants were tested for invariance using MGCFA and all were inadmissible for one of the two groups. Inspection of joint model differences in item loadings, scale reliabilities, scale inter-correlations established the extent of non-invariance. This paper discusses the implications of non-invariance within this particular study and identifies difficulties in usingan inventory in cross-cultural settings. It also provides suggestions about how to increase thelikelihood that a common factor structure can be recovered

Divergence in <it>cis-</it>regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

<p>Abstract</p> <p>Background</p> <p>Divergence within <it>cis</it>-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantitative genetic analysis suggests that <it>cis</it>-regulatory alleles near the <it>SWS2</it>-<it>LWS </it>opsins may contribute to this variation. Here, we sequence BACs containing the opsin genes of two cichlids, <it>Oreochromis niloticus </it>and <it>Metriaclima zebra</it>. We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate <it>cis</it>-regulatory sequences that influence cichlid opsin expression.</p> <p>Results</p> <p>We identified 20 conserved non-coding elements surrounding the opsins of cichlids and other teleosts, including one known enhancer and a retinal microRNA. Most conserved elements contained computationally-predicted binding sites that correspond to transcription factors that function in vertebrate opsin expression; <it>O. niloticus </it>and <it>M. zebra </it>were significantly divergent in two of these. Similarly, we found a large number of relevant transcription factor binding sites within each opsin's proximal promoter, and identified five opsins that were considerably divergent in both expression and the number of transcription factor binding sites shared between <it>O. niloticus </it>and <it>M. zebra</it>. We also found several microRNA target sites within the 3'-UTR of each opsin, including two 3'-UTRs that differ significantly between <it>O. niloticus </it>and <it>M. zebra</it>. Finally, we examined interspecific divergence among 18 phenotypically diverse cichlids from Lake Malawi for one conserved non-coding element, two 3'-UTRs, and five opsin proximal promoters. We found that all regions were highly conserved with some evidence of CRX transcription factor binding site turnover. We also found three SNPs within two opsin promoters and one non-coding element that had weak association with cichlid opsin expression.</p> <p>Conclusions</p> <p>This study is the first to systematically search the opsins of cichlids for putative <it>cis-</it>regulatory sequences. Although many putative regulatory regions are highly conserved across a large number of phenotypically diverse cichlids, we found at least nine divergent sequences that could contribute to opsin expression differences in <it>cis </it>and stand out as candidates for future functional analyses.</p